refactor: several changes related to code style and readability (#152)

* refactor: extract provision code extraction
* refactor: catch exceptions by type without later type check
* refactor: further code cleanup
* chore: log error with error level, not debug level

src/main/java/dev/dnpm/etl/processor/pseudonym/GpasPseudonymGenerator.java

@@ -23,8 +23,6 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.parser.IParser;
 import dev.dnpm.etl.processor.config.AppFhirConfig;
 import dev.dnpm.etl.processor.config.GPasConfigProperties;
-import java.net.URI;
-import java.net.URISyntaxException;
 import org.apache.commons.lang3.NotImplementedException;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.hc.core5.net.URIBuilder;
@@ -39,9 +37,11 @@ import org.springframework.http.*;
 import org.springframework.retry.support.RetryTemplate;
 import org.springframework.web.client.HttpClientErrorException.BadRequest;
 import org.springframework.web.client.HttpClientErrorException.Unauthorized;
-import org.springframework.web.client.RestClientException;
 import org.springframework.web.client.RestTemplate;
 
+import java.net.URI;
+import java.net.URISyntaxException;
+
 public class GpasPseudonymGenerator implements Generator {
 
     private final FhirContext r4Context;
@@ -52,10 +52,10 @@ public class GpasPseudonymGenerator implements Generator {
     private final RestTemplate restTemplate;
     private final @NotNull String genomDeTanDomain;
     private final @NotNull String pidPsnDomain;
-    protected final static String createOrGetPsn = "$pseudonymizeAllowCreate";
+    protected static final String CREATE_OR_GET_PSN = "$pseudonymizeAllowCreate";
-    protected final static String createMultiDomainPsn = "$pseudonymize-secondary";
+    protected static final String CREATE_MULTI_DOMAIN_PSN = "$pseudonymize-secondary";
-    private final static String SINGLE_PSN_PART_NAME = "pseudonym";
+    private static final String SINGLE_PSN_PART_NAME = "pseudonym";
-    private final static String MULTI_PSN_PART_NAME = "value";
+    private static final String MULTI_PSN_PART_NAME = "value";
 
     public GpasPseudonymGenerator(GPasConfigProperties gpasCfg, RetryTemplate retryTemplate,
         RestTemplate restTemplate, AppFhirConfig appFhirConfig) {
@@ -85,7 +85,7 @@ public class GpasPseudonymGenerator implements Generator {
         switch (domainType) {
             case SINGLE_PSN_DOMAIN -> {
                 final var requestBody = createSinglePsnRequestBody(id, pidPsnDomain);
-                final var responseEntity = getGpasPseudonym(requestBody, createOrGetPsn);
+                final var responseEntity = getGpasPseudonym(requestBody, CREATE_OR_GET_PSN);
                 final var gPasPseudonymResult = (Parameters) r4Context.newJsonParser()
                     .parseResource(responseEntity.getBody());
 
@@ -93,7 +93,7 @@ public class GpasPseudonymGenerator implements Generator {
             }
             case MULTI_PSN_DOMAIN -> {
                 final var requestBody = createMultiPsnRequestBody(id, genomDeTanDomain);
-                final var responseEntity = getGpasPseudonym(requestBody, createMultiDomainPsn);
+                final var responseEntity = getGpasPseudonym(requestBody, CREATE_MULTI_DOMAIN_PSN);
                 final var gPasPseudonymResult = (Parameters) r4Context.newJsonParser()
                     .parseResource(responseEntity.getBody());
 
@@ -150,23 +150,22 @@ public class GpasPseudonymGenerator implements Generator {
                 log.debug("API request succeeded. Response: {}", responseEntity.getStatusCode());
                 return responseEntity;
             }
-        } catch (RestClientException rce) {
+        } catch (BadRequest e) {
-            if (rce instanceof BadRequest) {
+            String msg = "gPas or request configuration is incorrect. Please check both."
-                String msg = "gPas or request configuration is incorrect. Please check both."
+                + e.getMessage();
-                    + rce.getMessage();
+            log.error(msg);
-                log.debug(
+            throw new PseudonymRequestFailed(msg, e);
-                    msg);
+        } catch (Unauthorized e) {
-                throw new PseudonymRequestFailed(msg, rce);
+            var msg = "gPas access credentials are invalid  check your configuration. msg:  '%s"
-            }
+                .formatted(e.getMessage());
-            if (rce instanceof Unauthorized) {
+            log.error(msg);
-                var msg = "gPas access credentials are invalid  check your configuration. msg:  '%s".formatted(
+            throw new PseudonymRequestFailed(msg, e);
-                    rce.getMessage());
+        }
-                log.error(msg);
+        catch (Exception unexpected) {
-                throw new PseudonymRequestFailed(msg, rce);
-            }
-        } catch (Exception unexpected) {
             throw new PseudonymRequestFailed(
-                "API request due unexpected error unsuccessful gPas unsuccessful.", unexpected);
+                "API request due unexpected error unsuccessful gPas unsuccessful.",
+                unexpected
+            );
         }
         throw new PseudonymRequestFailed(
             "API request due unexpected error unsuccessful gPas unsuccessful.");

src/main/kotlin/dev/dnpm/etl/processor/services/ConsentProcessor.kt

@@ -137,15 +137,7 @@ class ConsentProcessor(
             }
 
             val provisionComponent: ProvisionComponent = provisions.first()
-
+            val provisionCode = getProvisionCode(provisionComponent)
-            var provisionCode: String? = null
-            if (provisionComponent.code != null && provisionComponent.code.isNotEmpty()) {
-                val codableConcept: CodeableConcept = provisionComponent.code.first()
-                if (codableConcept.coding != null && codableConcept.coding.isNotEmpty()) {
-                    provisionCode = codableConcept.coding.first().code
-                }
-            }
-
             if (provisionCode != null) {
                 try {
                     val modelProjectConsentPurpose =
@@ -177,6 +169,17 @@ class ConsentProcessor(
         }
     }
 
+    private fun getProvisionCode(provisionComponent: ProvisionComponent): String? {
+        var provisionCode: String? = null
+        if (provisionComponent.code != null && provisionComponent.code.isNotEmpty()) {
+            val codableConcept: CodeableConcept = provisionComponent.code.first()
+            if (codableConcept.coding != null && codableConcept.coding.isNotEmpty()) {
+                provisionCode = codableConcept.coding.first().code
+            }
+        }
+        return provisionCode
+    }
+
     private fun setGenomDeSubmissionType(mtbFile: Mtb) {
         if (appConfigProperties.genomDeTestSubmission) {
             mtbFile.metadata.type = MvhSubmissionType.TEST
@@ -238,9 +241,9 @@ class ConsentProcessor(
             consent.provision.provision.filter { subProvision ->
                 isRequestDateInRange(requestDate, subProvision.period)
                 // search coding entries of current provision for code and system
-                subProvision.code.map { c -> c.coding }.flatten().firstOrNull { code ->
+                subProvision.code.map { c -> c.coding }.flatten().any { code ->
                     targetCode.equals(code.code) && targetSystem.equals(code.system)
-                } != null
+                }
             }.map { subProvision ->
                 subProvision
             }
@@ -257,11 +260,11 @@ class ConsentProcessor(
         researchAllowedPolicySystem: String?,
         policyRules: Collection<Coding>
     ): Boolean {
-        return policyRules.find { code ->
+        return policyRules.any { code ->
             researchAllowedPolicySystem.equals(code.getSystem()) && (researchAllowedPolicyOid.equals(
                 code.getCode()
             ))
-        } != null
+        }
     }
 
     fun isRequestDateInRange(requestDate: Date?, provPeriod: Period): Boolean {